I cant answer about it working with all the stock parts under the hood , but the directions that come with it says it will. Also it just filters dirt from my understanding , you still have your stock water separator/filter.
It fits with a stock truck but it's tight, also the Fleetguard filter that comes with the kit I had an issue with it hitting the throttle valve but it was very slight.
As far as filtering and water separation that would depend on the filter you run. The Cat filter is not a water seperator. I have 10k on this filter. I think I'll change it every 15 or 20k. No scientific reasons just personal gut feeling.
The kit is well worth it even if it's stock. CR injectors are very particular about clean fuel. Dirt and water is the enemy.
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